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In your case you will be using Transit virtual interface + Direct Connect gateway + Transit Gateway, the prefixes advertised to on-premises would be controlled via the allowed prefixes field under Direct Connect gateway.
In the allowed prefixes you can define the 3 subnets that you wish to establish the connectivity with on-premises., and on-premises will only receive those three subnets CIDRs.
Below are two guides goes through the same, https://repost.aws/knowledge-center/direct-connect-vpc-bgp https://docs.aws.amazon.com/directconnect/latest/UserGuide/allowed-to-prefixes.html#allowed-to-prefixes-transit-gateway
answered 3 years ago
Hello.
As you recognize, when route propagation is enabled, the CIDR of the VPC is advertised as the route.
However, we thought we could control communication with the on-premises by configuring routing to the Transit Gateway only in the route table of the subnet we want to communicate with the on-premises.
In other words, communication with on-premises is not possible unless a route destined to the Transit Gateway is set in the route table for the subnet that does not communicate with on-premises.
So we thought there would be no problem with advertising the VPC's CIDR to the on-premises route.
